How to Build CHD@ZJU

CHD related Articles were retrieved from Pubmed, by entering keywords "coronary heart disease" and constrict the publish date from 2000/1/1 to now (2013/1/23). As a result, totally 115898 articles were found and their abstracts were downloaded for text mining. Since some articles didn't contain abstracts, only 88396 abstracts remained.

The text-mining process to get CHD related genes could be divided in to 5 following steps:

  • 1) Extracting all keywords from abstracts and ignoring those keywords start with numbers. 101402 keywords were extracted.

  • 2) Input these keywords into Gene library in ArrayTrack and find possible related genes. 4674 genes were then found.

  • 3) Put these 4674 genes again into pubmed abstracts to find related aticles. Only genes which offical name or there keyword description (such as prolactin for gene PRL) could be found in the abstract would be remained. As a result, 1247 genes were remained.

  • 4) Manually examined on the 1247 genes to validate it was acutally related to CHD. Some genes would be filtered if it represents other meanings (such as gene CAD, Entrez ID:790, carbamoyl-phosphate synthetase 2, is mostly meant coronary arterial disease in articles). 681 genes were then validated with at least one reference.

  • 5) All genes was compared with 1078 CHD genes in RGD database, and 370 genes were overlapped. These 370 genes were labels as "RGD_Supported" and the other 293 genes were labels as "REFERED". All 663 genes had supported references in CHD@ZJU which were examined by step 4.
  • How To contact Us

    Collaboration Information: Prof. Xiaohui Fan (fanxh@zju.edu.cn)

    Website using assistance : Leihong Wu (11019004@zju.edu.cn)



    Basic Information

    Gene Name: CXCL12

    Description: chemokine (C-X-C motif) ligand 12 (stromal cell-derived factor 1)

    Entrez Gene ID: 6387

    SwissProt Acc Number: P48061

    RefSeq: NM_000609

    It was suspected to be CHD related:

    .."we conclude that fibrocytes, likely recruited through the CXCR4/CXCL12 axis, may contribute to the increase in the fibroblast population in CHD heart."..

    From PMID: 23177618, in Journal Pathol Res Pract , 2012


    References

    There were 17 potential papers with CXCL12 and CHD.

    PMIDTitleJournalsDetails
    23839111 Extracorporeal cardiac shock wave therapy ameliorates myocardial fibrosis by decreasing the amount of fibrocytes after acute myocardial infarction in pigs.Coronary artery diseaseMore Details
    23531450 Relationship between chemokine (C-X-C motif) ligand 12 gene variant (rs1746048) and coronary heart disease: case-control study and meta-analysis.GeneMore Details
    23177618 Fibrocytes are associated with the fibrosis of coronary heart disease."Pathology, research and practice"More Details
    23468663 RNAi-based functional profiling of loci from blood lipid genome-wide association studies identifies genes with cholesterol-regulatory function.PLoS geneticsMore Details
    22386691 Lack of association between the CXCL12 rs501120 polymorphism and cardiovascular disease in Spanish patients with rheumatoid arthritis.Human immunologyMore Details
    21804106 "Comparative analysis of genome-wide association studies signals for lipids, diabetes, and coronary heart disease: Cardiovascular Biomarker Genetics Collaboration."European heart journalMore Details
    22115649 Double-edged role of the CXCL12/CXCR4 axis in experimental myocardial infarction.Journal of the American College of CardiologyMore Details
    21242481 Genetic risk score and risk of myocardial infarction in Hispanics.CirculationMore Details
    22042884 Association of genetic variants and incident coronary heart disease in multiethnic cohorts: the PAGE study.Circulation. Cardiovascular geneticsMore Details
    22015231 Plasma levels of stromal cell-derived factor-1 in patients with coronary artery disease: effect of clinical presentation and cardiovascular risk factors.AtherosclerosisMore Details
    21764664 Transcriptional fingerprint of human whole blood at the site of coronary occlusion in acute myocardial infarction.EuroIntervention : journal of EuroPCR in collaboration with the Working Group on More Details
    21415067 The novel atherosclerosis locus at 10q11 regulates plasma CXCL12 levels.European heart journalMore Details
    21731663 Plasma chemokine levels are associated with the presence and extent of angiographic coronary collaterals in chronic ischemic heart disease.PloS oneMore Details
    22216278 Large scale association analysis identifies three susceptibility loci for coronary artery disease.PloS oneMore Details
    22137643 CXCL12: a new player in coronary disease identified through human genetics.Trends in cardiovascular medicineMore Details
    19059114 CXCL12 induction of inducible nitric oxide synthase in human CD8 T cells.The Journal of heart and lung transplantation : the official publication of theMore Details
    16456091 Molecular signatures determining coronary artery and saphenous vein smooth muscle cell phenotypes: distinct responses to stimuli."Arteriosclerosis, thrombosis, and vascular biology"More Details

    NOTEs: These result is mostly from TEXT-MINING and there might have mismatches.



    PPI interactions

    There were totally 10 unique genes interacted with CXCL12. Show PPI network

    Gene nameInteraction typereference PMIDCHD relation
    CXCL12 Co-crystal Structure10954912|10954912,9618518 CHD related
    CD4 in vitro10600606 CHD related
    MMP2 in vitro11571304 CHD related
    FN1 Reconstituted Complex11023498 CHD related
    PF4 Reconstituted Complex10233851 CHD related
    VCAN Reconstituted Complex11083865 CHD related
    CXCR4 Co-crystal Structure21757744 CHD related
    DPP4 in vitro11390394 CHD related
    CTSG in vitro;in vivo11241273 No
    ELANE in vitro12068293 CHD related


    Involved FDA drugs

    StatusDrubBank IDNameIndicationATC Code
    approvedDB06822TinzaparinTinzaparin is used for the prevention of postoperative venous thromboembolism in patients undergoing orthopedic surgery and in patients undergoing general surgery who are at high risk of developing postoperative venous thromboembolism. It is also used for the treatment of deep vein thrombosis and/or pulmonary embolism. It is indicated for use in preventing clot formation in indwelling intravenous lines for hemodialysis.B01AB10